@gaith I think their presence was explained well enough. They seemed to be a security force, and I got the impression that they did stealth ops mission stuff as well, kind of like Navy Seals in Starfleet. They provide the crew of the Enterprise with the additional security they need, but they are not Starfleet officers, so they don't do all of the science/exploration stuff. At least that's my understanding.

Sure they're explained, but that doesn't mean they're given context. Admiral Forrest calls them "military", thereby heavily implying that 'Fleeters aren't military, which has generally been a vague matter the franchise has avoided making any explicit statements on. Also, are these MACOs formally affiliated with Starfleet, or just on loan to the ship and its captain? If not, why doesn't Starfleet have a dedicated security service of its own (or are we really expected to believe that Malcolm's as good as it gets)? And if they're specifically needed for the Xindi Crisis, why do some stick around in S4? Etc.

As for Twilight, I enjoy it also, despite the nagging question of why the remaining humans didn't take the logical course of action of seeking sanctuary on Vulcan. And while I'm certainly an Archer/Polly guy, I wouldn't cite is as the definitive argument for their pairing, either.